Our long-term research on the biological significance of genomic sequences that readily adopt non-B DNA structures led us to discover a specialized sequence context in which DNA bases readily becomes unpaired under superhelical strain. We called sequences with such unusual physical properties base unpairing regions (BURs). We subsequently identified SATB1, a nuclear protein that recognizes and specifically binds in vivo to BUR DNA. During the last funding period, we uncovered a new dimension in mammalian gene regulation in which SATB1 folds chromatin into loops and simultaneously regulates a large number of genes. BURs of target gene loci are tethered onto the SATB1 protein network, which serves as an architectural platform to recruit transcriptional regulators and chromatin remodeling proteins to alter epigenetic states at target loci. Interestingly, we have observed such genome organizing activity to be closely associated with dramatic cellular changes, such as during T cell development, T cell activation, and acquisition of aggressive cancer phenotypes. Our next goals are proposed in four aims: 1) determine the roles of Satb1 post-translational modifications on functional chromatin organization and tumorigenesis, 2) determine genome organization underlying aggressive cancer, 3) study the biological function of mobile versus immobile SATB1 populations, and 4) identify and investigate the role of novel BUR-binding proteins in ES cells. These studies, connecting nuclear architecture and chromatin dynamics, will provide a new concept in gene regulation that underlies major changes in cellular phenotypes, such as during cancer progression and cell development.